356 IDENTIFICATION OF HBV DUAL INFECTION USING DIRECT SEQUENCING DATA

2011 ◽  
Vol 54 ◽  
pp. S143
Author(s):  
B. Beggel ◽  
M. Neumann-Fraune ◽  
G. Lawyer ◽  
R. Kaiser ◽  
J. Verheyen ◽  
...  
Keyword(s):  
Direct Sequencing ◽  
Dual Infection ◽  
Sequencing Data

scholarly journals Sequoia: an interactive visual analytics platform for interpretation and feature extraction from nanopore sequencing datasets

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ratanond Koonchanok ◽  
Swapna Vidhur Daulatabad ◽  
Quoseena Mir ◽  
Khairi Reda ◽  
Sarath Chandra Janga
Keyword(s):  
Single Molecule ◽  
Visual Analytics ◽  
Visual Analysis ◽  
Direct Sequencing ◽  
Visual Exploration ◽  
Nanopore Sequencing ◽  
Sequencing Data ◽  
Rna Sequences ◽  
Sequencing Technologies ◽  
Signal Features

Abstract Background Direct-sequencing technologies, such as Oxford Nanopore’s, are delivering long RNA reads with great efficacy and convenience. These technologies afford an ability to detect post-transcriptional modifications at a single-molecule resolution, promising new insights into the functional roles of RNA. However, realizing this potential requires new tools to analyze and explore this type of data. Result Here, we present Sequoia, a visual analytics tool that allows users to interactively explore nanopore sequences. Sequoia combines a Python-based backend with a multi-view visualization interface, enabling users to import raw nanopore sequencing data in a Fast5 format, cluster sequences based on electric-current similarities, and drill-down onto signals to identify properties of interest. We demonstrate the application of Sequoia by generating and analyzing ~ 500k reads from direct RNA sequencing data of human HeLa cell line. We focus on comparing signal features from m6A and m5C RNA modifications as the first step towards building automated classifiers. We show how, through iterative visual exploration and tuning of dimensionality reduction parameters, we can separate modified RNA sequences from their unmodified counterparts. We also document new, qualitative signal signatures that characterize these modifications from otherwise normal RNA bases, which we were able to discover from the visualization. Conclusions Sequoia’s interactive features complement existing computational approaches in nanopore-based RNA workflows. The insights gleaned through visual analysis should help users in developing rationales, hypotheses, and insights into the dynamic nature of RNA. Sequoia is available at https://github.com/dnonatar/Sequoia.

scholarly journals Genotyping hepatitis B virus dual infections using population-based sequence data

2012 ◽  
Vol 93 (9) ◽  
pp. 1899-1907 ◽  
Author(s):  
Bastian Beggel ◽  
Maria Neumann-Fraune ◽  
Matthias Döring ◽  
Glenn Lawyer ◽  
Rolf Kaiser ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Sequence Data ◽  
Synthetic Data ◽  
Dual Infection ◽  
Population Based ◽  
Model Verification ◽  
Sequencing Data ◽  
B Virus ◽  
Dual Infections

The hepatitis B virus (HBV) is classified into distinct genotypes A–H that are characterized by different progression of hepatitis B and sensitivity to interferon treatment. Previous computational genotyping methods are not robust enough regarding HBV dual infections with different genotypes. The correct classification of HBV sequences into the present genotypes is impaired due to multiple ambiguous sequence positions. We present a computational model that is able to identify and genotype inter- and intragenotype dual infections using population-based sequencing data. Model verification on synthetic data showed 100 % accuracy for intergenotype dual infections and 36.4 % sensitivity in intragenotype dual infections. Screening patient sera (n = 241) revealed eight putative cases of intergenotype dual infection (one A–D, six A–G and one D–G) and four putative cases of intragenotype dual infection (one A–A, two D–D and one E–E). Clonal experiments from the original patient material confirmed three out of three of our predictions. The method has been integrated into geno2pheno[hbv], an established web-service in clinical use for analysing HBV sequence data. It offers exact and detailed identification of HBV genotypes in patients with dual infections that helps to optimize antiviral therapy regimens. geno2pheno[hbv] is available under http://www.genafor.org/g2p_hbv/index.php.

scholarly journals Bartonella Infections in Deer Keds (Lipoptena cervi) and Moose (Alces alces) in Norway

2012 ◽  
Vol 79 (1) ◽  
pp. 322-327 ◽  
Author(s):  
Samuel Duodu ◽  
Knut Madslien ◽  
Eva Hjelm ◽  
Ylva Molin ◽  
Anna Paziewska-Harris ◽  
...  
Keyword(s):  
Alces Alces ◽  
Direct Sequencing ◽  
Single Species ◽  
Housekeeping Gene ◽  
Sequencing Data ◽  
Content Type ◽  
Spread Of Infection ◽  
Deer Ked

ABSTRACTInfections withBartonellaspp. have been recognized as emerging zoonotic diseases in humans. Large knowledge gaps exist, however, relating to reservoirs, vectors, and transmission of these bacteria. We describe identification by culture, PCR, and housekeeping gene sequencing ofBartonellaspp. in fed, wingless deer keds (Lipoptena cervi), deer ked pupae, and blood samples collected from moose,Alces alces, sampled within the deer ked distribution range in Norway. Direct sequencing from moose blood sampled in a deer ked-free area also indicatedBartonellainfection but at a much lower prevalence. The sequencing data suggested the presence of mixed infections involving two species ofBartonellawithin the deer ked range, while moose outside the range appeared to be infected with a single species.Bartonellawere not detected or cultured from unfed winged deer keds. The results may indicate that long-term bacteremia in the moose represents a reservoir of infection and thatL. cerviacts as a vector for the spread of infection ofBartonellaspp. Further research is needed to evaluate the role ofL. cerviin the transmission ofBartonellato animals and humans and the possible pathogenicity of these bacteria for humans and animals.

scholarly journals Molecular mechanisms of reversion to the ts+ (non-temperature-sensitive) phenotype of influenza A cold-adapted (ca) virus strains

2007 ◽  
Vol 88 (10) ◽  
pp. 2724-2729 ◽  
Author(s):  
T. M. Tsfasman ◽  
S. G. Markushin ◽  
I. I. Akopova ◽  
Y. Z. Ghendon
Keyword(s):  
Influenza A ◽  
Molecular Mechanisms ◽  
Direct Sequencing ◽  
Temperature Sensitive ◽  
Sequencing Data ◽  
Cold Adapted ◽  
Phenotypic Manifestation ◽  
Genes Encoding ◽  
Virus Strains ◽  
Temperature Sensitive Phenotype

A ts+ ca− (non-temperature-sensitive, non-cold-adapted) revertant of the A/Leningrad/134/47/57 ca strain influenza virus [A/Leningrad/134/47/ts+18/1957(H2N2)], obtained in our previous study, lost phenotypic manifestation of ts mutations by the PB2, NP and NS genes, although, according to sequencing data, it acquired only two true reversions of a mutation in the PB2 and PB1 genes. Direct sequencing showed the appearance of 27 additional mutations (13 coding) in the genes encoding the PB2, PB1, PA, NP, M and NS proteins of the revertant, along with the above-mentioned two true reversions. We conjecture that some of these mutations suppressed phenotypic manifestation of ts mutations in the NS and NP genes.

scholarly journals High frequency of NAT2 slow acetylator alleles in the Malay population of Indonesia: an awareness to the anti-tuberculosis drug induced liver injury and cancer

2017 ◽  
Vol 26 (1) ◽  
pp. 7-13 ◽  
Author(s):  
Retno W. Susilowati ◽  
Kinasih Prayuni ◽  
Intan Razari ◽  
Syukrini Bahri ◽  
Rika Yuliwulandari
Keyword(s):  
Direct Sequencing ◽  
Bimodal Distribution ◽  
Acetylator Phenotype ◽  
Sequencing Data ◽  
Drug Induced ◽  
Slow Acetylator ◽  
Nat2 Genotype ◽  
Nat2 Polymorphism ◽  
Specific Allele ◽  
Malay Population

Background: Arylamine N-acetyltransferase 2 (NAT2) polymorphism was previously reported to have association with the risk of drug toxicities and the development of various diseases. Previous research on the Indonesian population, especially Javanese and Sundanese, showed that there were 33% NAT2 slow acetylator phenotype. The aim of this study was to map the NAT2 variation in the Malay ethnic to gain a deeper insight into NAT2 haplotypic composition in this ethnic.Methods: 50 healthy samples from the Indonesian Malay ethnic were obtained. They were interviewed about their ethnic backgrounds for the last three generations. DNA was extracted from peripheral blood and NAT2 genotyping was done using the PCR direct Sequencing. Data were compiled according to the genotype and allele frequencies estimated from the observed numbers of each specific allele. Haplotype reconstruction was performed using PHASE v2.1.1 software.Results: We found 7 haplotypes consisting of 6 SNPs and 14 NAT2 genotype variations in Indonesian Malay population. The most frequent allele was NAT2*6A (38%) which was classified as a slow acetylator allele. According to bimodal distribution, the predicted phenotype of the Malay population was composed of 62% rapid acetylator and 38% slow acetylator. According to trimodal distribution, the predicted phenotypes for rapid, intermediate and slow acetylators were 10%, 52% and 38% respectively.Conclusion: Our result indicates the presence of the allelic distribution and revealed the most frequent acetylator status and phenotype for the Indonesian Malay population. The result of this study will be helpful for future epidemiological or clinical studies and for understanding the genetic basis of acetylation polymorphism in Indonesia.

scholarly journals High-Resolution Hepatitis C Virus Subtyping Using NS5B Deep Sequencing and Phylogeny, an Alternative to Current Methods

2014 ◽  
Vol 53 (1) ◽  
pp. 219-226 ◽  
Author(s):  
Josep Quer ◽  
Josep Gregori ◽  
Francisco Rodríguez-Frias ◽  
Maria Buti ◽  
Antonio Madejon ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Real Time ◽  
Deep Sequencing ◽  
Direct Sequencing ◽  
Treatment Strategies ◽  
Dual Infection ◽  
Genotype 1 ◽  
Hcv Genotype ◽  
Genotype Ii

Hepatitis C virus (HCV) is classified into seven major genotypes and 67 subtypes. Recent studies have shown that in HCV genotype 1-infected patients, response rates to regimens containing direct-acting antivirals (DAAs) are subtype dependent. Currently available genotyping methods have limited subtyping accuracy. We have evaluated the performance of a deep-sequencing-based HCV subtyping assay, developed for the 454/GS-Junior platform, in comparison with those of two commercial assays (Versant HCV genotype 2.0 and Abbott Real-time HCV Genotype II) and using direct NS5B sequencing as a gold standard (direct sequencing), in 114 clinical specimens previously tested by first-generation hybridization assay (82 genotype 1 and 32 with uninterpretable results). Phylogenetic analysis of deep-sequencing reads matched subtype 1 calling by population Sanger sequencing (69% 1b, 31% 1a) in 81 specimens and identified a mixed-subtype infection (1b/3a/1a) in one sample. Similarly, among the 32 previously indeterminate specimens, identical genotype and subtype results were obtained by direct and deep sequencing in all but four samples with dual infection. In contrast, both Versant HCV Genotype 2.0 and Abbott Real-time HCV Genotype II failed subtype 1 calling in 13 (16%) samples each and were unable to identify the HCV genotype and/or subtype in more than half of the non-genotype 1 samples. We concluded that deep sequencing is more efficient for HCV subtyping than currently available methods and allows qualitative identification of mixed infections and may be more helpful with respect to informing treatment strategies with new DAA-containing regimens across all HCV subtypes.

Incidence and significance of K-RAS mutation in first line treatment of colorectal cancer (cc): Experience of a single institution (Hospital Universitario Central de Asturias (HUCA))

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. e15081-e15081
Author(s):  
J. Vieitez ◽  
P. Jiménez Fonseca ◽  
M. Fernandez de Sanmamed ◽  
A. S. Pitiot ◽  
G. Crespo ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Clinical Data ◽  
Direct Sequencing ◽  
Stage Iv ◽  
Sequencing Data ◽  
First Line ◽  
Ras Gene ◽  
Mutant Type ◽  
Ras Mutation ◽  
Significant Difference

e15081 Background: Although the significance of K-RAS mutation and cetuximab/panitumumab has been established in first line (ASCO 08 abstract 2# and 4000#) and in previously treated patients (pts) (NEJM 2008; 359: 1757. JCO 2008; 26: 374. JCO 2008; 26: 1626), data of the significance of this mutation in relation to bevacizumab is scarcer (JNCI 2005; 97: 981). Methods: Sample tissue of alive patients diagnosed of stage IV colorectal cancer were analyzed for the presence of K-RAS mutation by PCR amplification and direct sequencing. Data regarding presence of K-RAS mutation were retrospectively analyzed in relation to clinical data. Results: From IV to XII 08 122 paraffin embedded samples were analyzed. The percentage of mutant cases were 41% (95% CI 32–51%). The most frequent mutant type was Gly12Asp (37%) followed by Gly12Val (25%) and Gly13Asp (19%). We have clinical data of 94 pts. 62 were men and 32 female. 25 pts had received previous complementary treatment; in 80 pts primary tumor was previously resected (85%); median number of affected organs was 1 (1–4); in first line 76 pts received bevacizumab and 18 did not received any biological agent. Response Rate (RR) between mutant and no mutant pts was 48% (95% CI 37–59%) vs 47.8% (95% CI 32–63%) (p=0.92). Median follow up was 15.4 months. Progression free survival was 15 months for mutant and native K-RAS. There were no differences in response or PFS in any subgroup studied. Multivariable Cox analysis did not find any significant difference between sex (p=0.78), primary resected organ (p=0.28), liver metastases (p=0.37), LDH value at diagnosis (p=0.0.43), employ of biological agents in first line (p=0.37) or mutation in K-RAS gene (p=0.68). Conclusions: The percentage of K-RAS mutants is coherent with the results of the literature; mutations Gly12Asp, Gly12Val, and Gly13Asp represents the majority of the cases (81%); no significant relation was found between responses or DFS and mutations in the gene. No significant financial relationships to disclose.

scholarly journals Exploring the Stony Coral Tissue Loss Disease Bacterial Pathobiome

2020 ◽  
Author(s):  
D.D. Iwanowicz ◽  
W.B. Schill ◽  
C. M. Woodley ◽  
A. Bruckner ◽  
K. Neely ◽  
...  
Keyword(s):  
Direct Sequencing ◽  
Bacterial Species ◽  
Tissue Loss ◽  
Coral Tissue ◽  
Coral Host ◽  
Dade County ◽  
Sequencing Data ◽  
Stony Coral ◽  
Clinically Normal ◽  
Diseased Coral

ABSTRACTA devastating novel coral disease outbreak, referred to as Stony Coral Tissue Loss Disease (SCTLD), was first described in 2014. It is thought to have originated offshore of Miami-Dade County, FL, but has persisted and spread, affecting new reefs along the Florida Reef Tract and reefs of at least 8 other Caribbean jurisdictions. We investigated the microbial communities of clinically normal and diseased specimens of five species of affected corals using targeted 16S ribosomal DNA sequencing (Illumina MiSeq). Fifty-nine bacterial sequences were identified using contrast analysis that had enriched abundance in diseased coral host microbiomes relative to the microbiomes of clinically normal hosts. Several sequences from known bacterial pathogens were identified in this group. Additionally, we identified fifty-three bacterial species that had differentially elevated numbers in clinically normal coral host samples relative to samples from diseased host corals. The bacterial consortia composing the clinically normal and diseased coral microbiomes were clearly distinct taxonomically. Predicted functional profiles based on taxonomy, however, were found to be quite similar. This indicates a high level of functional redundancy among diseased and clinically normal microbiome members. Further examination of the direct sequencing data revealed that while some bacteria were differentially distributed according to disease status, others were not. Fifty-one bacterial species were found in both diseased and clinically normal coral host samples and not differentially abundant in either disease state. These still may be important in explaining the presentation of disease.IMPORTANCEDetermining causation is a management top priority to guide control and intervention strategies for the SCTLD outbreak. Towards this goal we examined bacterial taxa that were differentially elevated in numbers in diseased corals as compared to clinically normal corals at Looe Key, FL in August 2018. Many of the bacterial species we detected are known to be pathogenic to humans, animals, and (or) plants, and some of these have been found associated with diseased corals in other studies. Microbes that were present (or conspicuous by their absence) in both diseased as well as clinically normal corals were also examined because “healthy” corals from a diseased location such as Looe Key may have been exposed but may not have been showing overt disease at the time of sampling. Although untangling of causation is not possible currently, certain bacterial cliques and excess nutrients appear to be potential risk factors in SCTLD pathology.

scholarly journals Using Oxford Nanopore Technology direct RNA sequencing to identify depurination events induced by ricin and other ribosome inactivating proteins

2021 ◽  
Author(s):  
Yan Ryan ◽  
Abbie Jasmine Harrison ◽  
Hannah Trivett ◽  
Catherine Hartley ◽  
Jonathan David ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Rna Sequencing ◽  
Direct Sequencing ◽  
Point Mutations ◽  
Ribosomal Subunit ◽  
Protein Translation ◽  
28S Rrna ◽  
Sequencing Data ◽  
Ribosome Inactivating Proteins ◽  
Oxford Nanopore

Depurination is a frequent modification to both DNA and RNA, in DNA causing point mutations through misincorporation, in RNA, disabling ribosomes and halting protein synthesis. Some modifications of nucleic acids can be determined by direct sequencing using Oxford Nanopore Technologies (ONT). However, the identification of modifications is often limited by noise and their variety and number. Ricin is a toxin which enters cells and depurinates an adenine base in the sarcin-ricin loop of the large ribosomal subunit. This leaves only a ribose backbone, thus inhibiting protein translation. In humans, biological threat agents and ribosome inactivating proteins, such as ricin and saporin, depurinate base 4605 on the 28S rRNA providing a single defined target to try and identify. We postulated that the depurination event could be detected using ONT direct RNA sequencing through a change in charge in the ricin loop. A software tool was developed, RIPpore, that quantified the adenine modification from direct RNA sequencing data of ribosomal RNA purified from respiratory epithelial cells exposed to ricin. This provided a novel method of directly identifying ricin exposure and a basis for the utility of ONT in detecting lesions in nucleic acids caused by depurination events.

High rate of prevalence of clock 3′UTR polymorphism rs1801260 and a novel variation: Association with diurnal preference

2011 ◽  
Vol 26 (S2) ◽  
pp. 1563-1563 ◽  
Author(s):  
B. Paul ◽  
G.M. McAlonan ◽  
M. Banerjee
Keyword(s):  
Indian Population ◽  
Direct Sequencing ◽  
Demographic Data ◽  
High Rate ◽  
Peak Performance ◽  
South Indian Population ◽  
Sequencing Data ◽  
South Indian ◽  
Diurnal Preference ◽  
Circadian Type

There are a number of reports which show CLOCK 3111 T/C SNP rs1801260 is associated with ‘eveningness’ circadian type, but the results are not consistent across different populations. The present study tried to address the effect of CLOCK polymorphisms on Diurnal preference in the South Indian population. 108 subjects were genotyped for rs1801260 polymorphism by direct sequencing. Demographic data was collected from genotypically stratified groups of subjects using a modified sleep wake cycle questionnaire. Data from the questionnaire recorded the subjects sleep wake pattern and their peak performance time of the day. The sequencing data was aligned and analyzed using Mutation Survey software for new mutations. We found a new variation in the 3′UTR region of the CLOCK gene (BankIt1368312 Seq1 HM626403, BankIt1368312 Seq2 HM626404) which may be a possible miRNA binding site. Our study found that CLOCK 3111 T/C polymorphism is negatively associated with Eveningness with a significance of 0.038. We found that the prevalence rate of rs1801260 is high and the ancestral genotype is associated with eveningness. Though the sample size was small this was a homogenous group from south India selected for the study. It is the first study in south Indian population to document the effect of CLOCK polymorphisms on Circadian rhythm.

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